scholarly journals From single bacterial cell imaging towards in vivo single-molecule biochemistry studies

2019 ◽  
Vol 63 (2) ◽  
pp. 187-196 ◽  
Author(s):  
Ulrike Endesfelder

Abstract Bacteria as single-cell organisms are important model systems to study cellular mechanisms and functions. In recent years and with the help of advanced fluorescence microscopy techniques, immense progress has been made in characterizing and quantifying the behavior of single bacterial cells on the basis of molecular interactions and assemblies in the complex environment of live cultures. Importantly, single-molecule imaging enables the in vivo determination of the stoichiometry and molecular architecture of subcellular structures, yielding detailed, quantitative, spatiotemporally resolved molecular maps and unraveling dynamic heterogeneities and subpopulations on the subcellular level. Nevertheless, open challenges remain. Here, we review the past and current status of the field, discuss example applications and give insights into future trends.

Cells ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 513 ◽  
Author(s):  
Chryssostomos Chatgilialoglu ◽  
Carla Ferreri ◽  
Nicholas E. Geacintov ◽  
Marios G. Krokidis ◽  
Yuan Liu ◽  
...  

Purine 5′,8-cyclo-2′-deoxynucleosides (cPu) are tandem-type lesions observed among the DNA purine modifications and identified in mammalian cellular DNA in vivo. These lesions can be present in two diasteroisomeric forms, 5′R and 5′S, for each 2′-deoxyadenosine and 2′-deoxyguanosine moiety. They are generated exclusively by hydroxyl radical attack to 2′-deoxyribose units generating C5′ radicals, followed by cyclization with the C8 position of the purine base. This review describes the main recent achievements in the preparation of the cPu molecular library for analytical and DNA synthesis applications for the studies of the enzymatic recognition and repair mechanisms, their impact on transcription and genetic instability, quantitative determination of the levels of lesions in various types of cells and animal model systems, and relationships between the levels of lesions and human health, disease, and aging, as well as the defining of the detection limits and quantification protocols.


2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Qian Peter Su ◽  
Wanqing Du ◽  
Qinghua Ji ◽  
Boxin Xue ◽  
Dong Jiang ◽  
...  

Abstract Intracellular membrane nanotube formation and its dynamics play important roles for cargo transportation and organelle biogenesis. Regarding the regulation mechanisms, while much attention has been paid on the lipid composition and its associated protein molecules, effects of the vesicle size has not been studied in the cell. Giant unilamellar vesicles (GUVs) are often used for in vitro membrane deformation studies, but they are much larger than most intracellular vesicles and the in vitro studies also lack physiological relevance. Here, we use lysosomes and autolysosomes, whose sizes range between 100 nm and 1 μm, as model systems to study the size effects on nanotube formation both in vivo and in vitro. Single molecule observations indicate that driven by kinesin motors, small vesicles (100–200 nm) are mainly transported along the tracks while a remarkable portion of large vesicles (500–1000 nm) form nanotubes. This size effect is further confirmed by in vitro reconstitution assays on liposomes and purified lysosomes and autolysosomes. We also apply Atomic Force Microscopy (AFM) to measure the initiation force for nanotube formation. These results suggest that the size-dependence may be one of the mechanisms for cells to regulate cellular processes involving membrane-deformation, such as the timing of tubulation-mediated vesicle recycling.


2015 ◽  
Vol 112 (32) ◽  
pp. E4390-E4399 ◽  
Author(s):  
Mathew Stracy ◽  
Christian Lesterlin ◽  
Federico Garza de Leon ◽  
Stephan Uphoff ◽  
Pawel Zawadzki ◽  
...  

Despite the fundamental importance of transcription, a comprehensive analysis of RNA polymerase (RNAP) behavior and its role in the nucleoid organization in vivo is lacking. Here, we used superresolution microscopy to study the localization and dynamics of the transcription machinery and DNA in live bacterial cells, at both the single-molecule and the population level. We used photoactivated single-molecule tracking to discriminate between mobile RNAPs and RNAPs specifically bound to DNA, either on promoters or transcribed genes. Mobile RNAPs can explore the whole nucleoid while searching for promoters, and spend 85% of their search time in nonspecific interactions with DNA. On the other hand, the distribution of specifically bound RNAPs shows that low levels of transcription can occur throughout the nucleoid. Further, clustering analysis and 3D structured illumination microscopy (SIM) show that dense clusters of transcribing RNAPs form almost exclusively at the nucleoid periphery. Treatment with rifampicin shows that active transcription is necessary for maintaining this spatial organization. In faster growth conditions, the fraction of transcribing RNAPs increases, as well as their clustering. Under these conditions, we observed dramatic phase separation between the densest clusters of RNAPs and the densest regions of the nucleoid. These findings show that transcription can cause spatial reorganization of the nucleoid, with movement of gene loci out of the bulk of DNA as levels of transcription increase. This work provides a global view of the organization of RNA polymerase and transcription in living cells.


Author(s):  
Timothy J. Hines ◽  
Cathleen Lutz ◽  
Stephen A. Murray ◽  
Robert W. Burgess

As sequencing technology improves, the identification of new disease-associated genes and new alleles of known genes is rapidly increasing our understanding of the genetic underpinnings of rare diseases, including neuromuscular diseases. However, precisely because these disorders are rare and often heterogeneous, they are difficult to study in patient populations. In parallel, our ability to engineer the genomes of model organisms, such as mice or rats, has gotten increasingly efficient through techniques such as CRISPR/Cas9 genome editing, allowing the creation of precision human disease models. Such in vivo model systems provide an efficient means for exploring disease mechanisms and identifying therapeutic strategies. Furthermore, animal models provide a platform for preclinical studies to test the efficacy of those strategies. Determining whether the same mechanisms are involved in the human disease and confirming relevant parameters for treatment ideally involves a human experimental system. One system currently being used is induced pluripotent stem cells (iPSCs), which can then be differentiated into the relevant cell type(s) for in vitro confirmation of disease mechanisms and variables such as target engagement. Here we provide a demonstration of these approaches using the example of tRNA-synthetase-associated inherited peripheral neuropathies, rare forms of Charcot-Marie-Tooth disease (CMT). Mouse models have led to a better understanding of both the genetic and cellular mechanisms underlying the disease. To determine if the mechanisms are similar in human cells, we will use genetically engineered iPSC-based models. This will allow comparisons of different CMT-associated GARS alleles in the same genetic background, reducing the variability found between patient samples and simplifying the availability of cell-based models for a rare disease. The necessity of integrating mouse and human models, strategies for accomplishing this integration, and the challenges of doing it at scale are discussed using recently published work detailing the cellular mechanisms underlying GARS-associated CMT as a framework.


2004 ◽  
Vol 215 ◽  
pp. 199-204 ◽  
Author(s):  
C. Aerts ◽  
R. Scuflaire ◽  
A. Thoul

In this contribution we review the current status of the determination of the rotational frequency in non-radially pulsating B stars, i.e. β Cep stars and slowly pulsating B stars. Considerable progress is currently being made in the understanding of the non-radial oscillations of main-sequence B stars by means of high-temporal, high-spatial resolution spectroscopic time series. This has led to the detection of frequency multiplets, which are interpreted as rotationally splitted non-radial modes and which allow an accurate determination of the surface rotational frequency in some stars. We outline how our future goal, i.e. the derivation of the internal rotation frequency, can be achieved.


Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1016 ◽  
Author(s):  
Deniz Streit ◽  
Thiruvenkadam Shanmugam ◽  
Asen Garbelyanski ◽  
Stefan Simm ◽  
Enrico Schleiff

Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.


2005 ◽  
Vol 8 (4) ◽  
pp. 463-473 ◽  
Author(s):  
Jean-Marc Schleich ◽  
Jean-Louis Dillenseger ◽  
Laurence Loeuillet ◽  
Jacques-Philippe Moulinoux ◽  
Claude Almange

Improvements in the diagnosis of congenital malformations explain the increasing early termination of pregnancies. Before 13 weeks of gestation, an accurate in vivo anatomic diagnosis cannot currently be made in all fetuses with current imaging instrumentation. Anatomopathologic examinations remain the gold standard to make accurate diagnoses, although they reach limits between 9 and 13 weeks of gestation. We present the first results of a methodology that can be applied routinely, using standard histologic section, thus enabling the reconstruction, visual estimate, and quantitative analysis of 13-week human embryonic cardiac structures. The cardiac blocks were fixed, embedded in paraffin, and entirely sliced by a microtome. One of 10 slices was topographically colored and digitized on an optical microscope. Cardiac volume was recovered by semiautomatic realignment of the sections. Another semiautomatic procedure allowed extracting and labeling of cardiac structures from the volume. Structures were studied with display tools, which disclosed the internal and external cardiac components and enabled determination of size, thickness, and precise positioning of ventricles, atria, and large vessels. This pilot study confirmed that a new 3-dimensional reconstruction and visualization method enables accurate diagnoses, including in embryos younger than 13 weeks. Its implementation at earlier stages of embryogenesis will provide a clearer view of cardiac development.


2013 ◽  
Vol 368 (1611) ◽  
pp. 20120355 ◽  
Author(s):  
Ken Ritchie ◽  
Yoriko Lill ◽  
Chetan Sood ◽  
Hochan Lee ◽  
Shunyuan Zhang

Bacteria, such as Escherichia coli and Caulobacter crescentus , are the most studied and perhaps best-understood organisms in biology. The advances in understanding of living systems gained from these organisms are immense. Application of single-molecule techniques in bacteria have presented unique difficulties owing to their small size and highly curved form. The aim of this review is to show advances made in single-molecule imaging in bacteria over the past 10 years, and to look to the future where the combination of implementing such high-precision techniques in well-characterized and controllable model systems such as E. coli could lead to a greater understanding of fundamental biological questions inaccessible through classic ensemble methods.


1960 ◽  
Vol 198 (4) ◽  
pp. 881-885 ◽  
Author(s):  
William J. Stekiel ◽  
John P. Kampine ◽  
Edward F. Banaszak ◽  
James J. Smith

The clearance and extraction by the liver of the dye, indocyanine green, was studied in dogs anesthetized with sodium pentobarbital (30 mg/kg). A simultaneous comparison ‘ in vivo’ indicated that within experimental error indocyanine space equals Evans blue space. Additional in vitro experiments suggest that indocyanine space is a reasonably satisfactory measure of plasma volume. Adequate mixing of the injected dye occurs within 2–3 minutes after injection. From 2 to 20 minutes after injection, the peripheral arterial and hepatic venous decay slopes are logarithmic and easily analyzable. Right hepatic vein concentrations of indocyanine were consistently higher (3.3%) than those of the left. Most of the assumptions made in the clearance-extraction principle of measuring hepatic flow are valid. At least two factors, the obtaining of representative hepatic venous samples and determination of true extraction ratio (because of hepatic circulatory time) represent ill-defined sources of error. The soundness of the clearance-extraction principle and unique characteristics of indocyanine make the single injection method a potentially useful tool for study of hepatic blood flow.


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